Practice Management Toolbox

Building a cancer genetics and prevention program


Gastroenterologists offer more than just high-quality colonoscopy for colon cancer prevention. We often are the specialists who first recognize a genetic cancer syndrome during our endoscopy or clinic sessions. The patient who piqued my interest in colon cancer genetics was a 24-year-old woman who was referred for postoperative nausea after a hysterectomy for early stage uterine cancer (that alone should have raised alarm bells). Endoscopy revealed (by happenstance) a stomach coated with polyps. This led to a colonoscopy and diagnosis of familial adenomatous polyposis (uterine cancer within FAP is unusual but reported, for those of you studying for boards). In 1991, no coordinated genetics program existed within my practice so I arranged referrals to genetic counselors, surgeons, and pathologists. This led to the discovery of FAP and early stage (and curable) cancers in her two brothers and her father, in addition to extended pedigree analysis that established multi-organ cancer risks in other relatives. Years later, she brought her two adopted children to meet me and told me of lighting candles in my honor during an American Cancer Society walk. This is why we become doctors.

In this column, Dr. Xavier Llor describes the cancer genetics program he and others have built at Yale. It provides practical steps that can be taken by health system or community-based gastroenterologists to recognize and manage these complex syndromes. We are the specialists on the front lines and Dr. Llor helps us provide the coordinated care our patients expect from us.

John I. Allen, MD, MBA, AGAF
Editor in Chief

Among all common cancers, breast and colon have the highest percentage of cases that are due to hereditary syndromes. Many of the responsible genes have been identified, and the last few years have seen an increase in uptake of genetic testing supported by the refinement of the clinical criteria suggestive of these syndromes as well as the clear improvement in outcomes as a result of the adoption of cancer preventive measures in mutation carriers.1 In spite of this, genetic testing for colorectal cancer (CRC) syndromes is not ordered as often as it should be according to the prevalence of these syndromes.2 In contrast, testing for hereditary breast cancer has become more generalized, and the threshold for ordering genetic testing in the latter is often lower than for CRC. The are several reasons for this: 1) much greater awareness, by both providers and the general public, of hereditary breast cancer conditions; 2) fewer providers with expertise in CRC genetics; 3) lack of a systematic approach to identify patients with potential CRC syndromes; and 4) absence of a clear premorbid phenotype for the most common of all CRC syndromes, Lynch syndrome.3

The recent recommendation in practice guidelines to screen all CRC tumors for Lynch syndrome either with immunohistochemistry to evaluate mismatch repair (MMR) protein expression or through tandem repeat analysis to test for microsatellite instability4 has highlighted that about 10% of all CRCs (a percentage consistently seen in different ethnic groups5) need further cancer genetic evaluation, and many will require sequencing of germline DNA. Although data on cost-effectiveness of this approach are somewhat conflicting,6,7 it is sensible because it is systematic, and studies have shown an increase in diagnostic yield through universal tumor screening.8 Unfortunately, in practice, often suspicious tumor testing results are not followed up by cancer genetics referrals, and many patients with CRC syndrome remain undiagnosed.

Patients with oligopolyposis (fewer than 100 polyps over time) also present diagnostic challenges. Some have attenuated familial adenomatous polyposis because of an APC mutation or MUTYH-associated polyposis. Recent findings have revealed other less commonly mutated genes that also result in oligopolyposis and a significant CRC risk: polymerases POLE and POLD1, GREM1, MCM9, or NTHL1. Because of the relatively low number of polyps in many of these syndromes and the lack of a systematic strategy to add up all polyps diagnosed over time, we not uncommonly fail to suspect some polyposis syndromes. Furthermore, the mixed pattern of polyps that is often associated with some of the mentioned mutated genes adds an extra challenge to diagnosing these cases.

Dr. Xavier Llor

Dr. Xavier Llor

Once individuals with CRC syndromes are identified, the challenge is to provide them with the care that they need, because many gastroenterologists, oncologists, and other health care providers are not extremely familiar with the current options for these patients.

In summary, there is a need to find systematic ways to triage and appropriately refer patients with a potential CRC syndrome to cancer genetics specialists so patients and their families can benefit from proper diagnosis and cancer preventive measures.

Building a comprehensive cancer genetics program

Although implementing systematic approaches is key to selecting individuals at risk, the complexity of caring for these patients demands a service that can stand up to the multiple challenges. For instance, most CRC syndromes are in fact multi-cancer syndromes with an increased risk of cancer and other pathologies in different organs beside the colon. Furthermore, the psychological implications of having a heritable cancer condition often take an important toll on affected families, with common feelings of guilt for having passed the mutated genes to the offspring.

Thus, to provide the best care to affected families, there is a tremendous need for well-organized and comprehensive cancer genetics services that are capable of responding to the multiple needs of these families so state-of-the-art cancer preventive measures can be carried out and multilevel support can be provided. The mentioned considerations were the guiding force in the creation of the Smilow Cancer Genetics and Prevention Program (SCGPP) at Yale. Thus, we established a comprehensive program that brings together health professionals specializing in different aspects of these patients’ care that ensures their proper attention in a longitudinal fashion, making the program their home for health care. We integrated in the program, among others, physician leaders in gastrointestinal (GI), breast, gynecological, endocrine, and genitourinary high-risk malignancies; genetic counselors; an advanced practice registered nurse specializing in cancer prevention and risk reduction; and a scientific director who leads the Clinical Laboratory Improvement Amendments–certified laboratory at Yale that offers in-house genetic testing, including full exome sequencing. The SCGPP was started in July 2015, and it currently provides more than 250 new consultations per month.

The following are several key elements that I consider important for a cancer genetics program and how they have been addressed at the SCGPP.

Identification through risk stratification

Because the identification of all individuals who can benefit from cancer genetics consultation is complex yet essential, a comprehensive approach with different strategies is often necessary.9 Universal tumor testing is an effective tool, but other complementary approaches such as the use of questionnaires can also contribute to identifying patients in need for cancer genetics assessment. In our program, the pathology department tests for MMR protein expression in all bowel and endometrial tumors. The ones that have loss of expression of an MMR protein are reported to the SCGPP, which contacts the patient’s providers to request a referral. In a relatively short implementation time, this has already resulted in a significant increase in the number of patients referred for cancer genetics consultation and new Lynch syndrome diagnosis. On the other hand, two brief and simplified questionnaires have been developed and distributed in clinics, one for health providers and one administered directly to patients. The questionnaires contain questions related to the patient’s own cancer history, polyp history, cancer screening tests, and family history. The first one assists health care providers in identifying individuals. The second one is completed by patients, collected, and reviewed by a genetic counselor. Suitable patients are invited to a cancer genetics consultation through their primary health care providers. A third questionnaire directed to endoscopy services will be rolled out soon. This collects information on completed endoscopy procedures, polyps and cancers found, and family history.

The program is currently working with information technology to develop a system to pull from the electronic medical record (EMR) relevant information on the patient’s own medical history, family history, and endoscopy findings. A set of criteria has been established so relevant information will generate an alert for prompt referral for the SCGPP.

Because education of health care providers about these conditions is essential to foster collaboration and to help them better understand about cancer risk assessment, genetics, and what the SCGPP can offer to some of their patients, sessions are routinely held with some of them to discuss different aspects on cancer genetics.

In summary, a comprehensive and coordinated approach is key to substantially expand the number of individuals identified and referred for cancer genetics assessment.

Genetic testing

During the last few years we have witnessed changes at different levels around genetic testing that are having a tremendous impact. Some of these changes pose significant new challenges that require rapid adaptation on the providers’ side. Thus, we are quickly moving from single gene testing to panels of genes tested at once. This has resulted in unexpected findings such as mutated genes not initially suspected or variants of unknown significance that often should be interpreted in the context of the personal and family history of cancer because of the lack of definite information on their potential pathogenicity.10 Adding to that, genome-scale tumor sequencing is becoming more common as it increasingly informs on the types of anti-tumor therapies to be selected for a specific patient (precision medicine). This approach is revealing some unexpected information because in some cases it has helped identify significant mutations in the germline.11

Finally, the increasing number of commercial laboratories offering genetic testing has resulted in more competition and lower prices, in some cases to a point that direct-to-consumer charges may be even lower than insurance copayments. This is contributing to a rapid increase in individuals being tested including patients who otherwise would unlikely have been tested in the past because of lack of fulfillment of insurance criteria. The challenge for us is to be ready to help navigate the increasing amount of information obtained as a result of all these changes.

Integration of electronic platforms

In an era of full implementation of EMRs, a cancer genetics program should not simply adapt to the new environment but fully embrace it and explore the possibilities that come with it. Thus, from its inception, the SCGPP has been embracing the electronic platforms to the maximum extent so the clinical operation is streamlined and documentation is well-displayed and accessible in the EMR. The Yale health care system uses EPIC (Epic Systems, Verona, WI) as its EMR, and the SCGPP uses Progeny (Progeny Genetics LLC, Delray Beach, FL) to collect data, construct family pedigrees, and build the research registry of the Program. A joint effort by the developers of both systems has resulted in integration at different levels. Thus, after a referral is received, patients are called, registered, and asked several questions including their own cancer and polyp history as well as their family history of cancer. This assists in triaging patients to the most appropriate SCGPP provider: a genetic counselor, a disease physician leader, or a combined visit according to the established internal protocol. In all cases, for new patients with GI cancer syndromes, a combined appointment of a genetic counselor and the GI physician leader is scheduled. At the same time, patients are sent an email with a link to the Progeny online questionnaire that includes personal and family history of cancer as well as extensive clinical information. Once the questionnaire is completed, the program generates a preliminary pedigree that patients can print, and the SCGPP gets a message communicating that the patient has completed this questionnaire. Therefore, when patients are seen on consultation, providers already have the provisional data and pedigree. During the visit, information is verified and edited as needed, and the finalized pedigree goes live through a hyperlink in the EMR. Every revision results in an updated pedigree visible through the mentioned hyperlink. This process saves a considerable amount of time to the providers and increases clinic efficiency.

Informed consent for the research registry is also fully electronic, with signatures recorded in tablets that transmit the signed document to a secure server.

The necessary team approach

Another essential component of a cancer genetics program like this is the integrated and comprehensive approach to patients. Thus, in our Program, the combined appointments for GI patients with the genetic counselor and the physician leader cover all different aspects of care, and a complete plan is suggested and discussed. Once the initial assessment is finalized and genetic testing results (if ordered) are completed, patients are followed prospectively to ensure that prophylactic and cancer prevention measures are undertaken according to the updated standards of care. Complex cases are discussed with the entire team in the weekly case conference that is always followed by a scientific conference with alternating topics such as journal club, practice improvement, ongoing research projects, and extensive case reviews.

Network integration

Although the needs for cancer genetics can be found in any corner of the map, it is not realistic to believe that services like this can be provided in a consistent fashion without being part of a bigger program umbrella. In our case, Yale’s Smilow Cancer Center charged the SCGPP with the duty to provide high quality and consistent cancer genetics services to the entire network that currently includes a total of 5 affiliated hospitals and 10 care centers. To do so, all cases seen outside the main campus are brought up for discussion in the weekly case conference. Furthermore, counselors distributed throughout the network routinely also see patients in the main office, and when away, they participate in case conference and scientific conference via teleconference or videoconference. All this is considered critical to facilitate a cohesive and state-of-the-art program that extends beyond the main campus. Recently, telemedicine is used to provide consultations directly to patients so the program’s services are brought to the most remote locations. A senior genetic counselor is in charge of the network operations to facilitate all these services and help engage providers in the corresponding facilities. She regularly attends tumor board meetings in the local hospitals to help disseminate knowledge in cancer genetics as well as to assist in the identification of patients who can benefit from referral to the SCGPP.

Surveillance and recall program

Key to the success of a cancer genetics program is successfully coordinating care so preventive tests and measures are performed to decrease cancer risk. The SCGPP aims to be the home for familial and hereditary cancer patients. For these patients, this implies a strong commitment to their needs, with a special emphasis on the appropriate prophylactic and cancer surveillance measures. The registry database provides an extremely useful tool to track scheduled tests and procedures and to generate reminders. The advanced practice registered nurse meticulously follows them and ensures proper completion and review. She follows up on the scheduling of the specific tests, reviews results once these tests are completed, and brings them back to discussion with the physician leader. She also follows up on incomplete tests and helps to bring down potential barriers in the performance of these tests. Another key aspect of her job consists of facilitating the assistance of psychological support or risk reduction through lifestyle changes, such as smoking cessation or weight reduction, to patients in need of such services.

Cancer genetics research

Key to an academic program in cancer genetics like this one is to facilitate the study of familial and syndromic cancers, including aspects such as phenotype characterization or the efficacy of chemopreventive approaches. To accomplish this, a patient registry is essential. Registries are extremely useful tools that facilitate data accrual and analysis. The SCGPP registry is based on the Progeny suite that incorporates not only clinical and pedigree building components but also the genotype and sample management systems (LAB and LIMS). Thus, a fully searchable and robust database and biological sample repository have been created, and all patients are approached about participating in this institutional review board–approved registry.

Cancer prevention in nonfamilial, nonsyndromic cases

Some nongenetic factors such as diet, physical activity, or toxic exposure seem to underlie the important differences seen in CRC incidence around the world.12 Thus, interventions at this level can potentially have a very high impact for cancer prevention in all individuals. In fact, even individuals with genetic mutations that carry a high risk for developing malignancies can see their risk modified by addressing lifestyle/environmental factors.13 Thus, the SCGPP has created tools for assessment and risk stratification that take the mentioned factors into account and create a roadmap for primary prevention. The tools include questionnaires on all environmental exposures, lifestyle factors, and medications the patient is exposed to and that can influence cancer risk. The information is reviewed in a special clinic session, and all services to help modify risk factors are offered to the patient.


There is a clear need for GI cancer genetics services to reach all patients who can benefit from them, and at the same time the field is rapidly growing in complexity. More than ever, these services demand a multidisciplinary approach, with experts leading the care of these patients in a coordinated fashion with the rest of the health care community. However, payers have not fully recognized these complexities, and some critical aspects such as genetic counseling services are not always properly reimbursed. As we shape up the present and future of health care that should be fully personalized and patient-centered, embracing new ways of delivering it, we need to engage all the players and help them understand what this takes and the rewards in the form of better outcomes that will come with it.


1. Kastrinos F., Stoffel E.M. History, genetics, and strategies for cancer prevention in Lynch syndrome. Clin Gastroenterol Hepatol. 2014;12:715-27 (quiz e41-e43).

2. Karlitz J.J., Hsieh M.C., Liu Y., et al. Population-based Lynch syndrome screening by microsatellite instability in patients </=50: prevalence, testing determinants, and result availability prior to colon surgery. Am J Gastroenterol. 2015;110:948-55.

3. Llor X. When should we suspect hereditary colorectal cancer syndrome? Clin Gastroenterol Hepatol. 2012;10:363-7.

4. Giardiello F.M., Allen J.I., Axilbund J.E., et al. Guidelines on genetic evaluation and management of Lynch syndrome: a consensus statement by the US Multi-society Task Force on colorectal cancer. Am J Gastroenterol. 2014;109:1159-79.

5. Berera S., Koru-Sengul T., Miao F., et al. Colorectal tumors from different racial and ethnic minorities have similar rates of mismatch repair deficiency. Clin Gastroenterol Hepatol. 2016;14:1163-71.

6. Mvundura M., Grosse S.D., Hampel H., et al. The cost-effectiveness of genetic testing strategies for Lynch syndrome among newly diagnosed patients with colorectal cancer. Genet Med. 2010;12:93-104.

7. Barzi A., Sadeghi S., Kattan M.W., et al. Comparative effectiveness of screening strategies for Lynch syndrome. J Natl Cancer Inst. 2015;107:1-9.

8. Moreira L., Balaguer F., Lindor N., et al. Identification of Lynch syndrome among patients with colorectal cancer. JAMA. 2012;308:1555-65.

9. Stoffel E.M., Kastrinos F. Familial colorectal cancer, beyond Lynch syndrome. Clin Gastroenterol Hepatol. 2014;12:1059-68.

10. Desmond A., Kurian A.W., Gabree M., et al. Clinical actionability of multigene panel testing for hereditary breast and ovarian cancer risk assessment. JAMA Oncol. 2015;1:943-51.

11. Parsons D.W., Roy A., Yang Y., et al. Diagnostic yield of clinical tumor and germline whole-exome sequencing for children with solid tumors. JAMA Oncol. 2016;([Epub ahead of print])

12. Aleksandrova K., Pischon T., Jenab M., et al. Combined impact of healthy lifestyle factors on colorectal cancer: a large European cohort study. BMC Med. 2014;12:168.

13. Movahedi M., Bishop D.T., Macrae F., et al. Obesity, aspirin, and risk of colorectal cancer in carriers of hereditary colorectal cancer: a prospective investigation in the CAPP2 study. J Clin Oncol. 2015;33:3591-7.

Dr. Llor is in the department of medicine and cancer center, Yale University, New Haven, Conn. He discloses no conflicts of interest.

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